diff --git a/CHANGELOG.md b/CHANGELOG.md index 1938928aad..4902462052 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -8,13 +8,24 @@ See also our [versioning policy](https://amici.readthedocs.io/en/latest/versioni BREAKING CHANGES -* The MATLAB interface has been removed. * `ReturnDataView.posteq_numsteps` and `ReturnDataView.posteq_numsteps` now return a one-dimensional array of shape `(num_timepoints,)` instead of a two-dimensional array of shape `(1, num_timepoints)`. * `ReturnDataView.posteq_status` and `ReturnDataView.preeq_status` now return `list[SteadyStateStatus]` instead of an `ndarray[int]` of shape `(1, 3)`. +* The following deprecated functionality has been removed: + * The complete MATLAB interface has been removed. + * `NonlinearSolverIteration::functional` has been removed, + use `NonlinearSolverIteration::fixedpoint` instead. + * The deprecated argument `log_as_log10` to `SbmlImporter.sbml2amici` and + `SbmlImporter.sbml2jax` has been removed. Just remove this argument, as + this never had any effect. + * Deprecated imports from `amici.petab.*` in `amici.petab.simulations` + have been removed. Import those functions directly from their respective + modules. + * The `force_compile` argument to `import_petab_problem` has been removed. + See the `compile_` argument. ## v0.X Series diff --git a/include/amici/defines.h b/include/amici/defines.h index 269d17d4c4..a437abd7b3 100644 --- a/include/amici/defines.h +++ b/include/amici/defines.h @@ -195,7 +195,6 @@ enum class LinearMultistepMethod { /** CVODES/IDAS Nonlinear Iteration method */ enum class NonlinearSolverIteration { - functional = 1, /** deprecated */ fixedpoint = 1, newton = 2 }; diff --git a/python/sdist/amici/petab/petab_import.py b/python/sdist/amici/petab/petab_import.py index e39f8797ae..5aa16b3d33 100644 --- a/python/sdist/amici/petab/petab_import.py +++ b/python/sdist/amici/petab/petab_import.py @@ -9,7 +9,6 @@ import os import shutil from pathlib import Path -from warnings import warn import amici import petab.v1 as petab @@ -82,17 +81,6 @@ def import_petab_problem( :return: The imported model. """ - if "force_compile" in kwargs: - if kwargs["force_compile"]: - compile_ = True - del kwargs["force_compile"] - warn( - "The `force_compile` option is deprecated, please use the " - "new `compile_` option, which also supports 'do not compile'.", - DeprecationWarning, - stacklevel=2, - ) - if petab_problem.model.type_id not in (MODEL_TYPE_SBML, MODEL_TYPE_PYSB): raise NotImplementedError( "Unsupported model type " + petab_problem.model.type_id diff --git a/python/sdist/amici/petab/simulations.py b/python/sdist/amici/petab/simulations.py index 5aa86b49a2..0ee04332d1 100644 --- a/python/sdist/amici/petab/simulations.py +++ b/python/sdist/amici/petab/simulations.py @@ -18,24 +18,14 @@ from .. import AmiciExpData, AmiciModel from ..logging import get_logger, log_execution_time -# some extra imports for backward-compatibility -# DEPRECATED: remove in 1.0 -from .conditions import ( # noqa # pylint: disable=unused-import - create_edata_for_condition, +from .conditions import ( create_edatas, - create_parameterized_edatas, fill_in_parameters, ) -from .parameter_mapping import ( # noqa # pylint: disable=unused-import +from .parameter_mapping import ( ParameterMapping, create_parameter_mapping, - create_parameter_mapping_for_condition, ) -from .util import ( # noqa # pylint: disable=unused-import - get_states_in_condition_table, -) - -# END DEPRECATED try: import pysb diff --git a/python/sdist/amici/sbml_import.py b/python/sdist/amici/sbml_import.py index 0294180237..a04e133b06 100644 --- a/python/sdist/amici/sbml_import.py +++ b/python/sdist/amici/sbml_import.py @@ -293,7 +293,6 @@ def sbml2amici( compute_conservation_laws: bool = True, simplify: Callable | None = _default_simplify, cache_simplify: bool = False, - log_as_log10: bool = None, generate_sensitivity_code: bool = True, hardcode_symbols: Sequence[str] = None, ) -> None: @@ -448,10 +447,6 @@ def sbml2amici( :param cache_simplify: See :meth:`amici.DEModel.__init__`. - :param log_as_log10: - This option is deprecated and will be removed in a future version. - Also, this option never had any effect on model import. - :param generate_sensitivity_code: If ``False``, the code required for sensitivity computation will not be generated. @@ -464,16 +459,6 @@ def sbml2amici( """ set_log_level(logger, verbose) - if log_as_log10 is not None: - # deprecated 04/2025 - warnings.warn( - "The `log_as_log10` argument is deprecated and will be " - "removed in a future version. This argument can safely be " - "dropped without replacement.", - category=DeprecationWarning, - stacklevel=2, - ) - ode_model = self._build_ode_model( observables=observables, event_observables=event_observables, @@ -521,7 +506,6 @@ def sbml2jax( compute_conservation_laws: bool = True, simplify: Callable | None = _default_simplify, cache_simplify: bool = False, - log_as_log10: bool = None, ) -> None: """ Generate and compile AMICI jax files for the model provided to the @@ -585,22 +569,9 @@ def sbml2jax( :param cache_simplify: see :meth:`amici.DEModel.__init__` - - :param log_as_log10: - This option is deprecated and will be removed in a future version. - Also, this option never had any effect on model import. """ set_log_level(logger, verbose) - if log_as_log10 is not None: - warnings.warn( - "The `log_as_log10` argument is deprecated and will be " - "removed in a future version. This argument can safely be " - "dropped without replacement.", - category=DeprecationWarning, - stacklevel=2, - ) - ode_model = self._build_ode_model( observables=observables, sigmas=sigmas,